Kemal Yaylali
1e46fff2ff
docs/blog/rarelens.tex builds a 10-page write-up covering the Nextflow DSL2 pipeline, the three execution backends behind one API call, the Argo and ArgoCD track, Terraform, the external systems integrated, the ranking, the benchmark and the model. It is deliberately as much an account of what was wrong as of what works: the components that scored evidence nobody had looked up, the missense AUROC that fell from 0.872 to 0.500 once allele frequency was removed, the ontology walk that silently dropped 399 terms, and the propagation change that measured slightly worse than what it replaced and was kept anyway with the numbers published. Figures come from one headless-browser script. Screenshots are of the running application; the six diagrams are hand-written HTML styled from the same palette, rendered by the same script. Keeping both in one place is what stops the article drifting from the system, and every number in a diagram has to be changed deliberately.
38 lines
4.1 KiB
HTML
38 lines
4.1 KiB
HTML
<!doctype html><meta charset="utf-8"><link rel="stylesheet" href="_base.css">
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<style>
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.bar { height:19px; border-radius:3px; background:var(--plum); }
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.bar.pes { background:var(--plum-soft); border:1px solid var(--plum); }
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.bar.base { background:var(--soft); }
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.brow { display:grid; grid-template-columns:210px 1fr 62px; align-items:center; gap:11px; margin-bottom:7px; font-size:12.5px; }
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.brow .lab { color:var(--soft); text-align:right; }
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.brow .val { font-family:var(--mono); font-size:11.5px; }
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.track { background:var(--paper); border-radius:3px; }
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</style>
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<div id="frame">
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<h1>Does the phenotype ranking actually work?</h1>
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<p class="sub">Every case in Monarch's Phenopacket Store: given a real patient's reported terms, where does the gene their authors diagnosed rank among all 5,269 HPO-annotated genes? Ties give a range — optimistic counts a tie as a win, pessimistic counts every tied gene as ahead.</p>
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<div style="font-size:12px;color:var(--soft);font-weight:600;text-transform:uppercase;letter-spacing:0.08em;margin:4px 0 9px">Causal gene ranked first (top-1), 10,178 published cases</div>
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<div class="brow"><div class="lab">optimistic</div><div class="track"><div class="bar" style="width:81.0%"></div></div><div class="val">81.0%</div></div>
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<div class="brow"><div class="lab">pessimistic</div><div class="track"><div class="bar pes" style="width:45.9%"></div></div><div class="val">45.9%</div></div>
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<div class="brow"><div class="lab">random baseline</div><div class="track"><div class="bar base" style="width:0.4%"></div></div><div class="val">0.02%</div></div>
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<div style="font-size:12px;color:var(--soft);font-weight:600;text-transform:uppercase;letter-spacing:0.08em;margin:20px 0 9px">Causal gene in the top ten</div>
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<div class="brow"><div class="lab">optimistic</div><div class="track"><div class="bar" style="width:87.2%"></div></div><div class="val">87.2%</div></div>
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<div class="brow"><div class="lab">pessimistic</div><div class="track"><div class="bar pes" style="width:69.7%"></div></div><div class="val">69.7%</div></div>
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<div style="height:22px"></div>
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<div class="row">
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<div class="box amber" style="flex:1"><div class="t">The benchmark is contaminated, and it must be said out loud</div><div class="d">The median causal gene already carries <em>every one</em> of its patient's terms, because HPO's gene annotations are curated from these same case reports. This measures how well the ranking retrieves a gene HPO has already been told about: an upper bound. A prospective number, on a patient whose gene nobody has annotated yet, would be lower, and this corpus cannot say by how much.</div></div>
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<div style="width:15px"></div>
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<div class="box" style="flex:1"><div class="t">Measuring my own changes, including the one that failed</div><div class="d">Information-content weighting and ontology propagation both replaced plain term counting. Asked whether they helped, the corpus said only one of them did — pessimistic figures, 6,485 cases with six or more terms:</div>
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<table style="width:100%;border-collapse:collapse;font-size:11.5px;margin-top:9px">
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<tr style="color:var(--soft)"><td style="padding:3px 0">count terms (original)</td><td style="text-align:right;font-family:var(--mono)">61.8%</td><td style="text-align:right;font-family:var(--mono)">0.682</td></tr>
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<tr style="color:var(--green);font-weight:600"><td style="padding:3px 0">+ information content</td><td style="text-align:right;font-family:var(--mono)">63.6%</td><td style="text-align:right;font-family:var(--mono)">0.706</td></tr>
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<tr style="color:var(--soft)"><td style="padding:3px 0">+ propagation</td><td style="text-align:right;font-family:var(--mono)">58.2%</td><td style="text-align:right;font-family:var(--mono)">0.653</td></tr>
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<tr><td style="padding:3px 0">+ both (shipped)</td><td style="text-align:right;font-family:var(--mono)">59.5%</td><td style="text-align:right;font-family:var(--mono)">0.670</td></tr>
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</table>
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<div class="d" style="margin-top:7px">Weighting earns its place. Propagation costs about what weighting gains — kept for a reason the documentation argues rather than assumes, with the table there so a reader can disagree.</div></div>
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</div>
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</div>
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